title: Ctrl_c7_Culture

description: NK cells treated with msurfeov2, and isolated from Culture

data_processing:
Raw sequencing data were demultiplexed and trimmed to the spacer sequences using Cutadapt v3.2 74. The spacers were then aligned to the reference sgRNA library using Bowtie v1.3.0 75, and aligned reads were compiled into a count matrix that was further analyzed using MaGeCK-RRA 34, with parameters of  norm-method = total,  and gene-lfc-method = alphamean.
Assembly: Custom gRNA library
Supplementary files format and content: Tab-delimited text files contain sgRNA and gene IDs in the first 2 columns, followed by sgRNA counts for each sample
Library strategy: DNA-seq

source_name: Culture

extract_protocol:
Genomic DNA was extracted from spleens, dissected tumors, and pre-injected cell pellets using the methods from a previously study 33. Briefly, each sample was put in a 15 mL Falcon tube and had 6 mL Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH adjusted to 8.0) and 30 μL of 20 mg/mL Proteinase K (Qiagen) added, then incubated at 55 °C overnight. After tissue digestion, 30 μL of 10 mg/mL RNase A (Qiagen) was added to the lysed sample and incubated at 37 °C for 30 min. Digested tissues were cooled on ice before adding 2 mL cold 7.5 M ammonium acetate (Sigma) to precipitate proteins. Samples were mixed thoroughly and then centrifuged at 4,000 x g at 4 °C for 15 min. The supernatant was moved to a new 15 mL Falcon tube, 6 mL 100% isopropanol was added, and samples were centrifuged at 4,000 x g at 4 °C for 10 min. Genomic DNA pellets were washed once with 70% ethanol, and then centrifuged at 4,000 x g at 4 °C for 5 min. The supernatant was discarded, and remaining ethanol was removed using a pipette. Genomic DNA was air dried for 30-60 min, and then resuspended in 0.5-1 mL nuclease-free water overnight at room temperature. For cell pellets, 100-200 μL QuickExtract solution (Epicentre) was directly added to cells and incubated at 65 °C for 30 min. For mouse lymph nodes, QIAmp Fast DNA Tissue Kit (Qiagen) was used for gDNA extraction following the manufacturer’s protocol.
Library readout was performed by nested PCR reactions to decrease the effect of PCR-amplification bias on the screen. The first-round PCR amplified the sgRNA sequence of the AAV-SB vector from genomic DNA (~2.5 μg per 50 μL reaction, 24 reactions per sample), and the second-round PCR added barcoded sequencing adapters (2 μL per 30 μL reaction, 6 reactions per sample). Primers for PCR#133: Forward: 5’-aatggactatcatatgcttaccgtaacttgaaagtatttcg-3’ Reverse: 5’- actcctttcaagacctagtcgacg-3’ Each round of PCR was performed using the following thermocycler conditions: 98 °C for 1 min, 25 cycles of (98 °C for 1s, 60 °C for 5 s, 72 °C for 12 s), and 72 °C for 2 min. All PCR reactions were performed using Phusion Flash High Fidelity Master Mix. The final PCR products were pooled and normalized for each biological sample before combining individual biological samples. The pooled product (150 ng per sample) was then gel purified from a 2% E-gel EX (Life Technologies) using the QiaQuick Gel Extraction kit (Qiagen). The purified, pooled library was then quantified with a gel-based method using the Low-Range Quantitative Ladder (Life Technologies), dsDNA High-Sensitivity Qubit (Life Technologies), BioAnalyzer (Agilent), and/or qPCR. Libraries were sequenced with 5-20% PhiX using an Illumina NovaSeq 4000 sequencer at the Yale Center for Genomic Analysis (YCGA).

value: msurfeome_v2 grna library


title: iWAT WT control for H2KO

status: Public on May 09 2024

type: SRA

city: Atlanta

first: Bingzhong

last: Xue

state: GA

address: 50 Decatur St. SE

department: Biology

country: USA

institute: Georgia State University

library_source: transcriptomic

data_processing:
Primary sequencing data was produced by Illumina HiSeqTM 2000, the original image data is transferred into sequence data via base calling (Illumina GA Pipeline v1.5), which is defined as raw data or raw reads and saved as FASTQ file.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Assembly: mm10
Supplementary files format and content: FPKM of each sample was provided in TXT file

molecule: total RNA

organism: Mus musculus

source_name: subcutaneous white fat

extract_protocol:
Subcutaneoues white fat pad were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

tag: tissue

value: subcutaneous white fat

tag: age

tag: genotype

value: WT

tag: treatment

value: 7 day cold exposure at 6 degreeC


title: iWAT WT control for AH2Tg


title: Ctrl_c6_Culture

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

library_source: other

molecule: other

value: Culture

tag: cell type

value: NK cells


title: GL261_m13_Spleen_PBS

description: NK cells treated with PBS, and isolated from Spleen

source_name: Spleen

value: Spleen

value: PBS


title: 1team-2

city: Xi’an

first: Shan

last: Huang

address: No.157, Xi Wu Road

country: China

institute: The Second Afﬁliated Hospital of Xi’an Jiaotong University

data_processing:
Agarose gel electrophoresis is used to detect the integrity of the total RNA samples.Agilent 2100 Bioanalyzer is used to assess the quality and concentration of sequencing libraries.  The NanoDrop ND-1000 is employed to measure the accurate concentration of the total RNA (abs 260) as well as protein contamination and other conditions (ratio abs260/abs230).
Quantitative analysis of gene expression is conducted at two levels: Gene Level and Transcript Level. Software such as StringTie calculates transcript abundance by aligning sequencing results to known transcriptomes.
Balgown is used for further computation, and the unit of expression quantity is represented by FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
A threshold is set to screen for differentially expressed genes and transcripts, which requires a 1.5-fold difference, a p-value < 0.05, and a mean FPKM value within the group > 0.5.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Esophagus

extract_protocol:
The extracted total RNA samples are subjected to agarose electrophoresis and Nanodrop quality inspection and quantification, followed by mRNA enrichment using oligo(dT) magnetic beads.1-2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA is first enriched for mRNA using the NEB Next® Poly(A) mRNA Magnetic Isolation Module (or rRNA is removed using the RiboZero Magnetic Gold Kit). The processed RNA product is then used to construct a library with the KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

value: Esophagus

tag: cell line

value: Esophageal squamous cell carcinoma

value: FGL1 overexpression


title: 0team-3


title: GL261_m12_Spleen_PBS


title: GL261_m10_Spleen

description: NK cells treated with msurfeov2, and isolated from Spleen


title: GL261_m11_Tumor

description: NK cells treated with msurfeov2, and isolated from Tumor

source_name: Tumor

value: Tumor


title: 1team-1


title: 0team-2


title: GL261_m11_Spleen


title: 0team-1


title: Stim_CALHM2_3

data_processing:
Paired-end reads were processed using Cutadapt 3.2, aligned to the human transcriptome using Kallisto v0.45.0, and imported in R using the EdgeR package.
Assembly: GRCh38 Gencode version 96
Supplementary files format and content: Tab-delimited text files contain transcript and gene IDs in the first 3 columns, followed by estimated transcript abundances of each sample

molecule: polyA RNA

source_name: Primary peripheral blood NK cells

extract_protocol:
The mRNA of AAVS1-KO and CALHM2-KO primary NK cells with or with cancer stimulations were extracted with RNeasy plus kit (Qiagen) according to manufacturer’s instruction.
The mRNA library preparations were performed using a NEBNext® Ultra™ RNA Library Prep Kit, and samples were multiplexed using barcoded primers provided by NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 2).

value: Primary peripheral blood NK cells

value: Stimulated CALHM2-KO


title: GL261_m9_Spleen


title: Stim_CALHM2_2


title: GL261_m10_Tumor


title: Stim_AAVS1_3

value: Stimulated AAVS1-KO


title: E0771_07dpi_tumor

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data were pre-processed with Cell Ranger v6.0.1 (10x Genomics) pipeline, using a standard pipeline that aligned reads to the mm10 mouse reference transcriptome and aggregated multiple datasets with the “agg” function.
Assembly: mm10 mouse reference from 10X Genomics website
Supplementary files format and content: Standard output files from Cell Ranger (matrix.mtx, barcodes.tsv, and features.tsv)

source_name: tumor

extract_protocol:
The mRNA of AAVS1-KO and CALHM2-KO primary NK cells with or with cancer stimulations were extracted with RNeasy plus kit (Qiagen) according to manufacturer’s instruction.
NK cells were normalized to 1,000 cells / μL. Standard volumes of cell suspension were used for 10X Genomics gene expression library preparation to achieve a targeted cell recovery of 10,000 cells.

value: tumor

tag: time

value: E0771 tumor


title: GL261_m9_Tumor

value: msurfeome_v2 grna library


title: Stim_CALHM2_1


title: GL261_m8_Spleen


title: E0771_07dpi_spleen

source_name: spleen

value: spleen


title: Stim_AAVS1_2


title: GL261_m8_Tumor


title: Ctrl_c5_Culture


title: B16F10_07dpi_spleen

value: B16F10 tumor


title: Stim_AAVS1_1


title: Unstim_CALHM2_3

value: Unstimulated CALHM2-KO


title: GL261_m7_Spleen


title: GL261_m7_Tumor


title: GL261_m6_Spleen


title: Unstim_CALHM2_2


title: Unstim_AAVS1_3

value: Unstimulated AAVS1-KO


title: Unstim_AAVS1_2


title: Unstim_CALHM2_1


title: GL261_m5_Spleen

value: NK cells


title: GL261_m6_Tumor


title: GL261_m5_Tumor


title: GL261_m4_Tumor


title: GL261_m3_Spleen

value: Spleen


title: Unstim_AAVS1_1


title: wildtype hESC 1 [HIWT-2-LCH8149]

city: Guangzhou

first: Manqi

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC (release 0.11.9) whose results were parsed with MultiQC (release 1.9). Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore (release 0.6.5; default parameter). Trimmed read pairs were aligned to genome with STAR (release 2.7.4a) according to different aims. For alignment of gene, the following command-line arguments were used: --outSAMmultNmax 1 --outFilterMultimapNmax 10; for repeat locus, the arguments included: --outFilterMultimapNmax 1000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 1000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350. We computed the number of mapping reads unambiguously attributed to each gene using the featureCounts package (release 2.0.0; default parameter). Multiple mapped reads were only considered once to quantify expression of repeat locus.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene raw counts for each sample.

source_name: H1 hESC

growth_protocol: H1 hESCs were maintained in PGM1 medium (CA1007500,cellapy) on Matrigel (354277,Corning)coated plates at 37℃ in hypoxic incubator. The medium was changed daily.

extract_protocol:
Total RNA was extracted using RNA purification kit (EZBioscience)
poly A mRNA was isolated and RNA-seq library was constructed using NEB Next UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual

value: H1 hESC

value: human embryonic stem cell

value: WT


title: TYW1 knockout hESC 4 [C5-LCH8147]

value: TYW1 knockout


title: wildtype hESC 2 [HIWT-LCH8146]


title: GL261_m4_Spleen


title: GL261_m3_Tumor

value: Tumor


title: TYW1 knockout hESC 3 [C5-2-LCH8150]


title: GL261_m2_Spleen


title: TYW1 knockout hESC 1 [C45-2-LCH8151]


title: GL261_m1_Spleen


title: GL261_m1_Tumor


title: PATISD AML, LV10 2441, 24 H

city: Palo Alto

first: Maria Grazia

last: Roncarolo

state: California

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

description:
PATISD_24H_2441
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger v6.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix files

source_name: Bone marrow aspirate

extract_protocol:
AML samples were FACS-sorted for scRNA-seq on day 0, and CD4IL10 cells were sorted after expansion protocol for scRNA-seq on day 0. Harvested T cells and remaining AML cells and were co-cultured for 24 hours at a 1:1 (E:T) ratio.  CD4IL10 cells and AML cells were sorted and adjusted to a 1:1 ratio to allow equal representation of AML and CD4IL10 cells in scRNA-seq data. This was repeated twice, so that each AML sample was co-cultured with T cells from two different donors. scRNA-seq was completed at Stanford Functional Genomics Facility (SFGF) using the Chromium Single Cell Gene Expression kit (10X Genomics, CA, USA) and Illumina Novaseq (Illumina Inc, CA, USA) sequencer according to manufacturer’s protocols.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics).

value: Bone marrow aspirate

value: AML


title: TYW1 knockout hESC 2 [C45-LCH8148]


title: Pano2_m9_Spleen_PBS

value: PBS


title: PATISD AML, LV10 072, 24 H

description:
PATISD_24H_072
10X Genomics


title: Pano2_m8_Spleen_PBS


title: PATISD AML, Day 0, Replicate 2

description:
PATISD_0H_2
10X Genomics

value: Day 0


title: PATISD AML, Day 0, Replicate 1

description:
PATISD_0H_1
10X Genomics


title: PARCHW AML, Day 0, Replicate 1

description:
PARCHW_0H_1
10X Genomics


title: Pano2_m7_Tumor


title: PARCHW AML, LV10 2441, 24 H

description:
PARCHW_24H_2441
10X Genomics


title: Pano2_m6_Tumor


title: PARCHW AML, LV10 072, 24 H

description:
PARCHW_24H_072
10X Genomics


title: PARCEV AML, LV10 2441, 24 H

description:
PARCEV_24H_2441
10X Genomics


title: PARCHW AML, Day 0, Replicate 2

description:
PARCHW_0H_2
10X Genomics


title: Pano2_m5_Spleen


title: Pano2_m5_Tumor


title: GL261_m2_Tumor


title: Pano2_m4_Spleen


title: PARCEV AML, Day 0, Replicate 2

description:
PARCEV_0H_2
10X Genomics


title: PARCEV AML, Day 0, Replicate 1

description:
PARCEV_0H_1
10X Genomics


title: PARCEV AML, LV10 072, 24 H

description:
PARCEV_24H_072
10X Genomics


title: Pano2_m3_Tumor


title: PAPZCL AML, LV10 2441, 24 H

description:
PAPZCL_24H_2441
10X Genomics


title: Pano2_m3_Spleen


title: Pano2_m2_Spleen


title: PAPZCL AML, LV10 072, 24 H

description:
PAPZCL_24H_072
10X Genomics


title: PAPZCL AML, Day 0, Replicate 2

description:
PAPZCL_0H_2
10X Genomics


title: Pano2_m2_Tumor


title: Pano2_m1_Spleen


title: Pano2_m1_Tumor


title: LV10 2441, Day 0

description:
LV10_2441
10X Genomics

source_name: Peripheral Blood

value: Peripheral Blood

value: CD4 T cells


title: Pano2_m7_Spleen

value: msurfeome_v2 grna library


title: LV10 072, Day 0

description:
LV10_072
10X Genomics


title: Ctrl_c4_Culture

value: Culture


title: Pano2_m6_Spleen


title: Ctrl_c3_Culture


title: PAPZCL AML, Day 0, Replicate 1

description:
PAPZCL_0H_1
10X Genomics


title: BT-549,Ctrl,day2,hic,rep2

city: Guangzhou City

first: Ru

last: Qiu

state: Guangdong Province

address: No. 74, 2nd Yat-sen Road, Yuexiu District

institute: Sun Yat-sen University

library_source: genomic

data_processing:
For Hi-C data, principal component analysis of the normalized Hi-C matrix at 100-kb resolution was used for identification of chromatin A/B compartments.
We determined the location and number of TADs and identified the locations of TAD borders using an insulation score algorithm based on normalized contact matrices at 40-kb resolution.
The intra-chromosome interactions at 10-kb resolution were determined by Ay’s Fit-Hi-C software. The interactions with P value < 0.01, FDR < 0.01 and contact count > 2 were considered to be significant.
Assembly: hg19
Supplementary files format and content: .hic

molecule: genomic DNA

growth_protocol: BT-549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Following cellular cross-linking with 1% formaldehyde and nuclei extraction in hypotonic solution, the genomic DNA was digested with restriction enzyme MboI (NEB) at 37 °C overnight and labelled with biotinylated nucleotides when the cohesive ends were filled. Then, blunt-end proximity ligation was performed with T4 DNA ligase (NEB) at 16 °C for 4 h. After decrosslinking with proteinase K (Thermo) at 65°C overnight, ligated DNA was purified by QIAamp DNA Mini Kit (Qiagen) and sheared to ~400 bp. Next, Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen) was used to pull down the biotin-marked ligation junctions. Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS) according to the manufacturer’s instructions.
The Hi-C library was generated using NEBNext Ultra™ II DNA library Prep Kit (NEB) according to the manufacturer’s instructions.

treatment_protocol: Nexturastat A was administrated with 5uM for 2 days

value: Epithelial cell, Breast, Triple-negative

value: DMSO


title: BT-549,Nexturastat A,day2,hic,rep1

value: Nexturastat A


title: BT-549,Nexturastat A,day2,hic,rep2


title: Ctrl_c2_Culture

value: NK cells


title: Ctrl_c1_Culture


title: BT-549,Ctrl,day2,hic,rep1


title: E0771_m11_Spleen

value: Spleen


title: MDA-MB231, TSA, Day2,rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (0.6.7)
The filtered reads were then aligned to the human reference genome (GRCh38) using STAR (v2.7.9a).
Gene-level read counts were obtained using featureCounts (2.0.3).
Differential expression analysis was performed using DESeq2 (v1.30.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: MDA-MB231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was prepared using RNA Library Prep Kit (Vazyme) for Illumina. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA Library Prep Kit (Vazyme) for Illumina following manufacturer's protocols.

treatment_protocol: Nexturastat A was administrated with 7.65uM for 2 days

value: Tubastatin A


title: Pano2_m4_Tumor


title: MDA-MB231, TSA, Day2,rep1

value: WT


title: MDA-MB231, HPOB, Day2,rep3

value: HPOB


title: E0771_m9_Tumor

value: Tumor


title: E0771_m9_Spleen


title: E0771_m8_Spleen


title: MDA-MB231, DMSO, Day2,rep3


title: E0771_m10_Tumor


title: E0771_m8_Tumor


title: E0771_m7_Spleen


title: E0771_m6_Spleen


title: MDA-MB231, DMSO, Day2,rep1


title: E0771_m6_Tumor


title: MDA-MB231, DMSO, Day2,rep2


title: MDA-MB231, shHDAC6-2, Day0,rep3

value: HDAC6 knockdown


title: MDA-MB231, shHDAC6-2, Day0,rep2


title: E0771_m5_Spleen


title: E0771_m10_Spleen


title: MDA-MB231, shHDAC6-1, Day0,rep3


title: E0771_m5_Tumor


title: MDA-MB231, TSA, Day2,rep2


title: E0771_m12_Spleen


title: E0771_m4_Tumor


title: E0771_m3_Spleen


title: MDA-MB231, HPOB, Day2,rep2


title: MDA-MB231, shHDAC6-1, Day0,rep1


title: MDA-MB231, shCtrl, Day0,rep3


title: MDA-MB231, shHDAC6-1, Day0,rep2


title: MDA-MB231, HPOB, Day2,rep1


title: MDA-MB231, shCtrl, Day0,rep2


title: E0771_m3_Tumor


title: MDA-MB231, shCtrl, Day0,rep1


title: E0771_m2_Spleen


title: E0771_m2_Tumor


title: E0771_m7_Tumor


title: MDA-MB231, Nexturastat A, Day2,rep1


title: E0771_m1_Spleen


title: E0771_m1_Tumor


title: MDA-MB231, Ctrl, Day2,rep2


title: MDA-MB231, shHDAC6-2, Day0,rep1


title: MDA-MB231, Ctrl, Day2,rep1


title: B16F10_m11_Spleen


title: MDA-MB231,shHDAC6,ATAC,rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (0.6.7)
The filtered reads were then aligned to the human reference genome (GRCh38) using bowtie2 (v2.4.4).
The resulting BAM files were sorted and indexed using samtools (v1.13) and subsequently converted to bigwig files using deepTools (v3.5.1) for visualization in IGV (v4.1.0).
Peaks were called using MACS2 (v2.2.7.1).
The resulting peak files were annotated with gene information using ChIPseeker (v1.28.2).
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol: Genomic DNA was prepared using In-Situ ChIP Library Prep Kit (Vazyme) and ATAC-Seq Library Prep Kit for Illumina (Vazyme) for Illumina. 100000 cells were prepared for each ChIP-seq and ATAC-Seq.


title: E0771_m4_Spleen


title: MDA-MB231,shHDAC6,ATAC,rep2


title: B16F10_m9_Spleen


title: B16F10_m8_Spleen


title: B16F10_m8_Tumor


title: B16F10_m7_Tumor


title: MDA-MB231,shCtrl,ATAC,rep1


title: MDA-MB231,shCtrl,ATAC,rep3


title: MDA-MB231,Nexturastat A,ATAC,rep3


title: MDA-MB231,Nexturastat A,ATAC,rep2


title: B16F10_m6_Spleen


title: MDA-MB231,Nexturastat A,ATAC,rep1


title: MDA-MB231, Nexturastat A, Day2,rep2


title: B16F10_m7_Spleen


title: MDA-MB231,Ctrl,ATAC,rep3


title: MDA-MB231,Ctrl,ATAC,rep2


title: B16F10_m5_Spleen


title: B16F10_m5_Tumor


title: MDA-MB231,Ctrl,ATAC,rep1


title: B16F10_m10_Spleen


title: B16F10_m6_Tumor


title: B16F10_m4_Spleen


title: B16F10_m4_Tumor


title: B16F10_m9_Tumor


title: B16F10_m3_Spleen


title: MDA-MB231,shHDAC6,PolII,Rpb1 CTD,CST,rep2

tag: chip antibody

value: Rpb1 CTD (4H8) Mouse mAb (CST,Cat#2629)


title: MDA-MB231,shHDAC6,ATAC,rep1


title: B16F10_m3_Tumor


title: MDA-MB231,shCtrl,PolII,Rpb1 CTD,CST,rep1


title: B16F10_m2_Spleen


title: MDA-MB231,shCtrl,ATAC,rep2


title: MDA-MB231,shCtrl,PolII,input


title: B16F10_m2_Tumor


title: MDA-MB231,shHDAC6,PolII,input


title: MDA-MB231,Nexturastat A,Rpb1 CTD,CST,rep2


title: B16F10_m1_Tumor


title: B16F10_m1_Spleen


title: K7M2 tibia tumor

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: K7M2 tibia tumor

data_processing:
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/epithelial)
Assembly: mm10
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

source_name: tibia tumor

extract_protocol:
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10XGenomics, PN-1000121) according to the manufacturer's instructions
Libraries were constructed per 10x protocols

value: tibia tumor


title: MDA-MB231,Nexturastat A,Rpb1 CTD,CST,rep1


title: MDA-MB231,Ctrl,Rpb1 CTD,CST,rep2


title: F420 tibia tumor

description: F420 tibia tumor


title: MDA-MB231,Ctrl,Rpb1 CTD,CST,rep1


title: K7M2 lung metastasis

description: K7M2 lung metastasis

source_name: lung tumor

value: lung tumor


title: MDA-MB231,Nexturastat A,input


title: MDA-MB231,Ctrl,input


title: F420 lung metastasis

description: F420 lung metastasis


title: MDA-MB231,shCtrl,PolII,Rpb1 CTD,CST,rep2


title: MDA-MB231,Nexturastat A,Pan-acetyl,abcam,rep2

value: Anti-Histone H3 (acetyl K9 + K14 + K18 + K23 + K27) (abcam,Cat#ab47915)


title: MDA-MB231,shHDAC6,PolII,Rpb1 CTD,CST,rep1


title: MDA-MB231,Nexturastat A,Pan-acetyl,abcam,rep1


title: MDA-MB231,Ctrl,Pan-acetyl,abcam,rep2


title: spinal cord, nic symptomatic, rep3

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

country: Italy

institute: University of Rome Tor Vergata

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted to fastq files using bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw counts

source_name: spinal cord

extract_protocol:
Total RNA was extracted using Direct-zolTM RNA MiniPrep (ZYMO RESEARCH). 125ng of total RNA was used for the construction of sequencing libraries.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: spinal cord

value: B6.CgTg(SOD1G93A)1Gur/J strain

value: 20 mg/kg niclosamide


title: MDA-MB231,Ctrl,Pan-acetyl,abcam,rep1

value: Epithelial cell, Breast, Triple-negative


title: spinal cord, veh symptomatic, rep3

value: vehicle


title: MDA-MB231,Nexturastat A,panAc,input


title: spinal cord, nic symptomatic, rep1


title: MDA-MB231,Ctrl,panAc,input


title: spinal cord, veh symptomatic, rep2


title: spinal cord, veh symptomatic, rep1


title: MDA-MB231,shHDAC6,HDAC6,Novus,rep2

value: HDAC6 (Novus,Cat#NB100-56343)


title: spinal cord, nic end stage, rep4


title: spinal cord, nic end stage, rep3


title: spinal cord, nic end stage, rep2


title: MDA-MB231,shHDAC6,HDAC6,Novus,rep1


title: MDA-MB231,Ctrl,HDAC6,cut&tag,Novus,rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (0.6.7)
The filtered reads were then aligned to the human reference genome (GRCh38) using bowtie2 (v2.4.4).
The resulting BAM files were sorted and indexed using samtools (v1.13) and subsequently converted to bigwig files using deepTools (v3.5.1) for visualization in IGV (v4.1.0).
Peaks were called using MACS2 (v2.2.7.1).
The resulting peak files were annotated with gene information using ChIPseeker (v1.28.2).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: Cut&Tag


title: BALB/C control lung

description: BALB/C control lung

source_name: lung

value: lung


title: MDA-MB231,shHDAC6,HDAC6,negative control


title: spinal cord, nic end stage, rep1


title: spinal cord, veh end stage, rep4


title: spinal cord, veh end stage, rep3


title: MDA-MB231,Nexturastat A,HDAC6,Novus,rep2


title: MDA-MB231,Ctrl,HDAC6,Novus,rep2


title: MDA-MB231,Ctrl,HDAC6,input


title: MDA-MB231,Nexturastat A,HDAC6,CST,rep1

value: HDAC6 (CST,Cat#7558)


title: spinal cord, veh end stage, rep2


title: spinal cord, nic symptomatic, rep2


title: C57BL/6 control lung

description: C57BL/6 control lung


title: iPSC-EC, DSCAM +/+/+, rep 5

city: Boston

first: Vi

middle: T

last: Tang

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to the hg38 Human Genome using Spliced Transcripts Alignment to a Reference (STAR).
Transcript counts were computed using FeatureCount and normalized to the total number of reads per kilobase of exon per million (RPKM).
Assembly: hg38
Supplementary files format and content: groupexpr file contain raw and normalized transcript counts for each sample.

growth_protocol: iPSCs were maintained in mTeSR1 and differentiated into endothelial cells. iPSC-ECs were maintained in EGM2 medium.

extract_protocol:
cells were homogenized in Trizol Reagent (Life Technologies, Inc., Grand Island, NY) with TissueLyzer II (QIAGEN, Inc., Valencia, CA) and RNA was isolated by conventional methods. RNA went through two rounds of mRNA purification (polyA-selection) using Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad, CA). Double-stranded cDNA was generated using the Superscript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA).
The cDNA products were used to construct libraries with the Nextera XT DNA Sample Preparation Kit (Illumina, Inc., San Diego, CA).
Libraries were paired-end sequenced with a read length of 75 base pairs (75PE) on the Illumina NoaSeq 600.

value: iPSCs

value: Endothelial cells

value: DSCAM +/+/+


title: MDA-MB231,Nexturastat A,HDAC6,input


title: MDA-MB231,Ctrl,HDAC6,CST,rep1


title: spinal cord, veh end stage, rep1


title: WA232 Ascl4 CA1

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned to Ensembl GRCm38 reference transcriptome (Version-86), using the STAR aligner with the following parameters: trimLeft = 10, minTailQuality = 15, minAverageQuality = 20 and minReadLength = 30. Gene counts were calculated using HTSeq  (Data-no_QC-counts.tsv and Data-counts.tsv)
Cells that passed quality control were normalized (Data-normed.tsv)
Differential gene expression was analyzed using edgR.
Assembly: GRCm38.p4
Supplementary files format and content: Data-no_QC-counts.tsv; raw counts, all cells
Supplementary files format and content: Data-counts.tsv; raw counts, cells passed QC
Supplementary files format and content: Data-normed.tsv; normalized counts, cells passed QC

source_name: hippocampal neurons

extract_protocol: single cell extraction via patch pipette (patch-RNAseq)

value: hippocampal neurons

value: Nex-Cre


title: iPSC-EC, DSCAM -/+/+, rep 5

value: DSCAM -/+/+


title: WA235 Ascl4 CA1

description:
Data-no_QC-counts.tsv
Data-counts.tsv
Data-normed.tsv


title: WA228 Ascl4 CA1


title: WA230 Ascl4 CA1


title: WA233 Ascl4 CA1


title: WA234 Ascl4 CA1


title: WA229 Ascl4 CA1


title: MDA-MB231,Ctrl,HDAC6,cut&tag,Novus,rep2


title: iPSC-EC, DSCAM -/-/-, rep 4

value: DSCAM -/-/-


title: WA227 Ascl4 CA1


title: iPSC-EC, DSCAM -/+/+, rep 4


title: iPSC-EC, DSCAM -/-/-, rep 5


title: iPSC-EC, DSCAM -/-/+, rep 5

value: DSCAM -/-/+


title: iPSC-EC, DSCAM -/-/+, rep 4


title: iPSC-EC, DSCAM -/+/+, rep 3


title: iPSC-EC, DSCAM -/-/-, rep 3


title: WA223 Ascl4 CA1


title: WA224 Ascl4 CA1


title: iPSC-EC, DSCAM -/+/+, rep 2


title: WA231 Ascl4 CA1


title: WA226 Ascl4 CA1


title: WA222 Ascl4 CA1


title: iPSC-EC, DSCAM -/+/+, rep 1


title: WA219 Ascl4 CA1


title: iPSC-EC, DSCAM +/+/+, rep 3


title: iPSC-EC, DSCAM -/-/-, rep 2


title: WA221 Ascl4 CA1


title: WA220 Ascl4 CA1


title: iPSC-EC, DSCAM -/-/-, rep 1


title: WA217 Ascl4 CA1


title: WA216 Ascl4 CA1


title: iPSC-EC, DSCAM -/-/+, rep 2


title: iPSC-EC, DSCAM -/-/+, rep 1


title: WA218 Ascl4 CA1


title: iPSC-EC, DSCAM +/+/+, rep 2


title: WA215 GFP CA1

value: AAV-EGFP


title: WA213 GFP CA1


title: iPSC-EC, DSCAM +/+/+, rep 1


title: WA214 GFP CA1


title: WA212 GFP CA1


title: WA211 GFP CA1


title: naRNA-seq of LCLs, NA19257

city: Chicago

first: Carlos F

last: Buen Abad Najar

state: Illinois

address: 920 E 58th St

department: Medicine

institute: University of Chicago

description:
naRNA.counts.tab
naRNA.PSI.tab
naRNA.qqnorm.tab
naRNA.PSI_qqnorm.tab

data_processing:
For naRNA-seq, reads were aligned to the genome using STAR 2.7.7a with WASP mode and soft trimming.
naRNA-seq read counts were obtained from the BAM files using featureCounts.
Splice junction counts were obtained from the BAM files using regtools. Intron clusters were obtained with Leafcutter.
Counts were transformed first into counts per million (CPM) across each sample. log2 CPM counts (or percent spliced in for splicing data) were then normalized with standard normalization for each gene. Finally, we used rank normalization acros each sample to enforce normality to the distribution.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for naRNA-seq data
Supplementary files format and content: tab-delimited text file includes normalized counts for naRNA-seq data
Supplementary files format and content: tab-delimited text file includes percent spliced in for naRNA-seq data
Supplementary files format and content: tab-delimited text file includes normalized percent spliced in for naRNA-seq data

molecule: nuclear RNA

growth_protocol: LCLs were grown in RPMI + glutamine + Penn/Strep + 20% FBS. Cells were grown in 4 batches, with approximately 20-35 cell lines per batch.

extract_protocol:
For naRNA-seq, nuclei were isolated through a sucrose cushion followed by high-salt washes to dissociate nucleoplasm and weakly bound RNAs and proteins from chromatin.
rRNA was depleted using Lexogen ribocop v2 kit according to the manufacturer’s protocol. RNA was harvested with NEB Ultra Directional II RNA-seq kits.

value: Lymphoblastoid cell lines (LCLs)


title: naRNA-seq of LCLs, NA19247


title: iPSC-EC, DSCAM -/-/+, rep 3


title: iPSC-EC, DSCAM +/+/+, rep 4


title: WA209 GFP CA1


title: naRNA-seq of LCLs, NA19236


title: WA208 GFP CA1


title: WA207 GFP CA1


title: naRNA-seq of LCLs, NA19225


title: WA205 GFP CA1


title: naRNA-seq of LCLs, NA19213


title: WA210 GFP CA1


title: naRNA-seq of LCLs, NA19238


title: naRNA-seq of LCLs, NA19239


title: WA204 GFP CA1


title: WA206 GFP CA1


title: naRNA-seq of LCLs, NA19214


title: naRNA-seq of LCLs, NA19210


title: WA203 GFP CA1


title: naRNA-seq of LCLs, NA19207


title: naRNA-seq of LCLs, NA19203


title: WA202 GFP CA1


title: naRNA-seq of LCLs, NA19206


title: WA199 GFP CA1


title: WA200 GFP CA1


title: WA201 GFP CA1


title: naRNA-seq of LCLs, NA19201


title: naRNA-seq of LCLs, NA19200


title: naRNA-seq of LCLs, NA19198


title: WA198 GFP CA1


title: naRNA-seq of LCLs, NA19209


title: WA196 GFP CA1


title: WA197 GFP CA1


title: naRNA-seq of LCLs, NA19190


title: naRNA-seq of LCLs, NA19184


title: WA194 GFP CA1


title: naRNA-seq of LCLs, NA19160


title: WA195 GFP CA1


title: WA193 GFP CA1


title: naRNA-seq of LCLs, NA19153


title: naRNA-seq of LCLs, NA19152


title: WA190 GFP CA1


title: WA191 GFP CA1


title: WA189 GFP CA1


title: naRNA-seq of LCLs, NA19147


title: naRNA-seq of LCLs, NA19150


title: WA187 GFP CA1


title: WA188 GFP CA1


title: naRNA-seq of LCLs, NA19143


title: WA192 GFP CA1


title: naRNA-seq of LCLs, NA19140


title: WA185 GFP CA1


title: WA186 GFP CA1


title: naRNA-seq of LCLs, NA19146


title: naRNA-seq of LCLs, NA19141


title: WA184 GFP CA1


title: naRNA-seq of LCLs, NA19131


title: naRNA-seq of LCLs, NA19137


title: naRNA-seq of LCLs, NA19171


title: WA182 GFP CA1


title: naRNA-seq of LCLs, NA19130


title: WA181 GFP CA1


title: naRNA-seq of LCLs, NA19122


title: WA178 Ascl4 CA1


title: naRNA-seq of LCLs, NA19127


title: WA180 Ascl4 CA1


title: WA179 Ascl4 CA1


title: naRNA-seq of LCLs, NA19128


title: naRNA-seq of LCLs, NA19121


title: naRNA-seq of LCLs, NA19118


title: WA177 Ascl4 CA1


title: naRNA-seq of LCLs, NA19117


title: WA175 Ascl4 CA1


title: naRNA-seq of LCLs, NA19138


title: naRNA-seq of LCLs, NA19114


title: WA173 Ascl4 CA1


title: WA176 Ascl4 CA1


title: naRNA-seq of LCLs, NA19107


title: WA172 Ascl4 CA1


title: naRNA-seq of LCLs, NA19108


title: WA174 Ascl4 CA1


title: WA183 GFP CA1


title: WA171 Ascl4 CA1


title: naRNA-seq of LCLs, NA19102


title: naRNA-seq of LCLs, NA19101


title: WA170 Ascl4 CA1


title: naRNA-seq of LCLs, NA19099


title: WA169 Ascl4 CA1


title: WA167 Ascl4 CA1


title: naRNA-seq of LCLs, NA19098


title: WA168 Ascl4 CA1


title: WA166 Ascl4 CA1


title: WA164 Ascl4 CA1


title: naRNA-seq of LCLs, NA19096


title: naRNA-seq of LCLs, NA19095


title: naRNA-seq of LCLs, NA19092


title: naRNA-seq of LCLs, NA19093


title: WA165 Ascl4 CA1


title: naRNA-seq of LCLs, NA19119


title: WA162 Ascl4 CA1


title: WA161 Ascl4 CA1


title: WA163 Ascl4 CA1


title: naRNA-seq of LCLs, NA18934


title: WA160 GFP CA1


title: naRNA-seq of LCLs, NA18923


title: naRNA-seq of LCLs, NA18917


title: WA159 GFP CA1


title: naRNA-seq of LCLs, NA18924


title: WA158 GFP CA1


title: naRNA-seq of LCLs, NA18913


title: WA157 GFP CA1


title: naRNA-seq of LCLs, NA18910


title: naRNA-seq of LCLs, NA18915


title: WA155 GFP CA1


title: WA156 GFP CA1


title: naRNA-seq of LCLs, NA18909


title: naRNA-seq of LCLs, NA18881


title: WA154 GFP CA1


title: naRNA-seq of LCLs, NA18879


title: naRNA-seq of LCLs, NA18877


title: WA153 GFP CA1


title: WA152 GFP CA1


title: WA151 GFP CA1


title: naRNA-seq of LCLs, NA18870


title: naRNA-seq of LCLs, NA18876


title: naRNA-seq of LCLs, NA18868


title: WA149 GFP CA1


title: naRNA-seq of LCLs, NA18867


title: WA148 GFP CA1


title: naRNA-seq of LCLs, NA18864


title: naRNA-seq of LCLs, NA18862


title: naRNA-seq of LCLs, NA18858


title: naRNA-seq of LCLs, NA18853


title: WA146 GFP CA1


title: naRNA-seq of LCLs, NA18852


title: naRNA-seq of LCLs, NA18523


title: WA147 GFP CA1


title: WA144 GFP CA1


title: WA141 GFP CA1


title: WA142 GFP CA1


title: WA140 Ascl4 CA1


title: WA139 Ascl4 CA1


title: WA138 Ascl4 CA1


title: naRNA-seq of LCLs, NA18516


title: naRNA-seq of LCLs, NA18519


title: WA136 Ascl4 CA1


title: naRNA-seq of LCLs, NA18511


title: naRNA-seq of LCLs, NA18510


title: WA150 GFP CA1


title: WA134 Ascl4 CA1


title: naRNA-seq of LCLs, NA18508


title: naRNA-seq of LCLs, NA18507


title: WA133 Ascl4 CA1


title: WA132 Ascl4 CA1


title: WA145 GFP CA1


title: naRNA-seq of LCLs, NA18505


title: WA131 Ascl4 CA1


title: naRNA-seq of LCLs, NA18504


title: naRNA-seq of LCLs, NA18502


title: WA129 Ascl4 CA1


title: naRNA-seq of LCLs, NA18520


title: WA128 Ascl4 CA1


title: naRNA-seq of LCLs, NA18498


title: naRNA-seq of LCLs, NA18497


title: naRNA-seq of LCLs, NA18486


title: naRNA-seq of LCLs, NA18522


title: WA124 Ascl4 CA1


title: WA127 Ascl4 CA1


title: H3K36ME3 Cut&Tag of LCLs, NA19257

data_processing:
Cut&Tag reads were aligned to the genome using HISAT 2.2.1.
H3K36ME3 counts overlapping gene bodies were obtained using bedtools multicov.
Counts were transformed first into counts per million (CPM) across each sample. log2 CPM counts were then normalized with standard normalization for each gene. Finally, we used rank normalization acros each sample to enforce normality to the distribution.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for Cut&Tag data
Supplementary files format and content: tab-delimited text file includes normalized counts for Cut&Tag data
Library strategy: Cut&Tag

growth_protocol: LCLs were grown in RPMI + glutamine + Penn/Strep + 20% FBS. Cells were grown in 4 batches, with approximately 20-35 cell lines per batch. For Cut&Tag, 100,000 cells were frozen in 10% DMSO.

extract_protocol:
Cut&Tag was performed as described in DOI: dx.doi.org/10.17504/protocols.io.z6hf9b6 using polyclonal antibodies.
14 PCR cycles were performed for amplification.

tag: antibody


title: H3K36ME3 Cut&Tag of LCLs, NA19247


title: WA123 Ascl4 CA1


title: H3K36ME3 Cut&Tag of LCLs, NA19238


title: WA122 Ascl4 CA1


title: WA121 Ascl4 CA1


title: H3K36ME3 Cut&Tag of LCLs, NA19239


title: WA120 Ascl4 GC

value: GC


title: WA119 Ascl4 GC


title: WA130 Ascl4 CA1


title: WA118 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19225


title: H3K36ME3 Cut&Tag of LCLs, NA19214


title: WA117 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19223


title: WA135 Ascl4 CA1


title: H3K36ME3 Cut&Tag of LCLs, NA19213


title: WA126 Ascl4 CA1


title: naRNA-seq of LCLs, NA18499


title: WA125 Ascl4 CA1


title: H3K36ME3 Cut&Tag of LCLs, NA19210


title: WA114 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19209


title: H3K36ME3 Cut&Tag of LCLs, NA19207


title: WA112 Ascl4 GC


title: WA111 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19206


title: WA110 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19236


title: H3K36ME3 Cut&Tag of LCLs, NA19201


title: H3K36ME3 Cut&Tag of LCLs, NA19203


title: WA108 Ascl4 GC


title: WA109 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19200


title: WA107 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19195


title: H3K36ME3 Cut&Tag of LCLs, NA19196


title: WA106 Ascl4 GC


title: D24ONC201_3

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM33 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: brain tumor

growth_protocol: XFM cells were growth in DMEM medium supplemented with 10% FBS. A total of 1,000 cells were implanted into the pons and treatments were performed.

extract_protocol:
Tumor tissue was recovered as precisely as possible and immediately frozen using liquid nitrogen. Then, RNA was extracted from tissue using the RNeasy mini kit from Qiagen, following the manufacturer's instruction.
RNA concentration and quality were measured using a Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 TapeStation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 8. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instructions. Briefly, poly(A)-containing RNA molecules were selected and purified using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs were fragmented and reverse transcribed into a first cDNA strand using random primers. The second cDNA strand was synthesized in the presence of dUTP to ensure strand specificity. The resulting cDNA fragments were purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments were purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 TapeStation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). A total of 20-30 million paired-end reads (100 bp; Rd1:51; Rd2:51) were sequenced for each sample. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Vehicle- and ONC201-mice were intratumorally injected PBS; whereas D24 and D24ONC were treated with 10^7 pfu/mice at day 3 from cell implantation. ONC201 (in ONC201- and D24ONC-treated mice) was administered at 125 mg/kg at day 5 from cell implantation.

value: brain tumor

value: XFM cells implanted in brain

value: murine DMG cell line


title: WA116 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19190


title: D24ONC201_2


title: D24ONC201_1


title: WA113 Ascl4 GC


title: WA104 Ascl4 GC


title: WA103 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA19184


title: D24_1


title: ONC201_3


title: D24_2


title: H3K36ME3 Cut&Tag of LCLs, NA19171


title: ONC201_2


title: ONC201_1


title: H3K36ME3 Cut&Tag of LCLs, NA19198


title: H3K36ME3 Cut&Tag of LCLs, NA19160


title: vehicle_3

value: vehicle


title: WA101 Ascl4 GC


title: WA100 GFP GC


title: vehicle_1


title: WA105 Ascl4 GC


title: F. columnare challenge hour24 white bass rep6 gill tissue

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using  FastQC (v.0.11.8) and Trimmomatic (v.0.38). This was used to trim low-quality ends from reads and for Illumina adapter removal.
All reads were filtered for the removal of 18S, 5.8S, and 28S sequences using the STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) for alignment of sequences to the Morone 18S, 5.8S, and 28S sequences available on GenBank and output of unaligned reads used for subsequent analysis. This was completed as QC indicated the sequence reads WB-1-t4hr and HB-4-t4hr had 52.68% and 68.99% alignment to these sequences, respectively. These individuals were dropped from subsequent analysis.
The STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) were used to align all filtered reads generated for the other 46 samples to the white bass transcriptome using default parameters.
Read-counts were generated using the default parameters of HTSeq (v.0.9.0).
Gene expression fold-changes were determined between groups were determined in a pairwise fashion using edgeR (v.3.28.0) with TMM (Weighted trimmed mean of M-values) as the normalization method, Exact Test, and “robust” filter to strengthen estimations against potential outliers.
Assembly: All RNA transcripts from the white bass transcriptome shotgun assembly GAZY00000000.1 (GAZY01000001-GAZY01183659) in GenBank
Supplementary files format and content: tab-deliminated text file of read counts representing the total number of reads aligned to each genomic feature

organism: Morone chrysops

source_name: gill

growth_protocol: Fingerling white bass (WB) and hybrid striped bass (HB) (N=480 total, 240 of each) randomly selected from populations spawned indoors and reared in ponds to 2-3 months of age at the Harry K Dupree Stuttgart National Aquaculture Research Center (Stuttgart, Arkansas, USA) and stocked into 16 total replicate 18 L tanks (8 tanks for WB and 8 for HB, n=30 fish per tank). Fish were fed to apparent satiation 3 days per week, for 2 weeks prior to the study. Fish were not fed on the day before bacterial challenge or thereafter.

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

treatment_protocol: White bass (WB) and hybrid striped bass (HB) in the control group (t0hr) were given a mock treatment and sampled immediately prior to aquaria being challenged with 10 mL culture of Flavobacterium columnare isolate LSU-066-04 (0.70 absorbance at 550nm; 6.3X10^6 CFU/mL). Water was provided through the ultra-low-flow water delivery system at a rate of 30 ml/min for 24h then flow was increased to 200 mL/min. Fish were observed twice daily for the recording and removal of any dead or moribund fish, and fish were formally sampled at three timepoints after the challenge had been initiated, 1 hour post treatment (t1hr), 4 hours post treatment (t4hr), and 24 hours post treatment (t24hr).

tag: animal

value: white bass (WB)

value: gill

value: Flavobacterium columnare immersion

value: 24 hr after immersion


title: D24_3


title: WA099 GFP GC


title: F. columnare challenge hour1 white bass rep6 gill tissue

value: 1 hr after immersion


title: F. columnare challenge hour4 white bass rep6 gill tissue

value: 4 hr after immersion


title: H3K36ME3 Cut&Tag of LCLs, NA19152


title: F. columnare challenge hour24 white bass rep5 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19153


title: H3K36ME3 Cut&Tag of LCLs, NA19150


title: F. columnare challenge hour1 white bass rep5 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19147


title: F. columnare challenge hour4 white bass rep5 gill tissue


title: WA096 GFP GC

value: hippocampal neurons


title: F. columnare challenge hour0 white bass rep6 gill tissue

value: control mock immersion

value: 0 hr after mock treatment


title: WA098 GFP GC


title: vehicle_2


title: WA102 Ascl4 GC


title: WA097 GFP GC


title: F. columnare challenge hour4 white bass rep4 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19159


title: H3K36ME3 Cut&Tag of LCLs, NA19146


title: F. columnare challenge hour1 white bass rep4 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19143


title: F. columnare challenge hour0 white bass rep4 gill tissue


title: WA095 GFP GC


title: F. columnare challenge hour24 white bass rep3 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19141


title: WA093 GFP GC


title: F. columnare challenge hour1 white bass rep3 gill tissue


title: F. columnare challenge hour0 white bass rep3 gill tissue


title: F. columnare challenge hour0 white bass rep5 gill tissue


title: WA092 GFP GC


title: F. columnare challenge hour24 white bass rep2 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19138


title: F. columnare challenge hour24 white bass rep4 gill tissue


title: F. columnare challenge hour4 white bass rep2 gill tissue


title: WA091 GFP GC


title: F. columnare challenge hour1 white bass rep2 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19137


title: WA090 GFP GC


title: F. columnare challenge hour0 white bass rep2 gill tissue


title: F. columnare challenge hour24 white bass rep1 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19131


title: WA089 GFP GC


title: F. columnare challenge hour4 white bass rep1 gill tissue


title: F. columnare challenge hour1 white bass rep1 gill tissue


title: H3K36ME3 Cut&Tag of LCLs, NA19130


title: WA094 GFP GC


title: F. columnare challenge hour0 white bass rep1 gill tissue


title: DIPGIV_ONC201_3

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode v43 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: SU-DIPG IV

growth_protocol: Pediatric glioma CHLA-03-AA cell line was obtained from American Type Culture Collection (ATCC, Manassas, VA), and was maintained with Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12) (Gibco) supplemented with B-27 Supplement (Gibco), basic fibroblast growth factor and epidermal growth factor (20 ng/mL Sigma-Aldrich, St Louis, USA). SJ-GBM2 was obtained from Children’s Oncology Group and was maintained in Iscove’s Modified Dulbecco’s Medium supplemented with 20% fetal bovine serum (FBS), 4 mM L-glutamine and 1X insulin-transferrin-selenium ITS (Gibco). TP54 (H3.3K27M) and SU-DIPG IV (H3.1K27M) cell lines were maintained as neurospheres cultured in a specialized medium for expansion of human neural stem and progenitor cells (NeuroCultTM NS-A Proliferation Kit, #05751, STEMCELL Technologies), basic fibroblast growth factor and epidermal growth factor (20 ng/mL Sigma-Aldrich, St Louis, USA). All media were supplemented at 1% penicillin/streptomycin. All the cell lines were maintained in a humidified atmosphere containing 5% CO2 at 37 °C, were routinely tested for mycoplasma (Mycoalert mycoplasma detection kit; Lonza) and authenticated at the CIMA Genomic Core Facility (Pamplona, Spain) using DNA profiling.

extract_protocol:
Total RNA was isolated using the RNeasy® Mini Kit (Qiagen), including DNase digestion, following the manufacturer’s instructions and recommendations.
RNA was subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 8. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). 20-30 million pair-end reads (100 bp; Rd1:51; Rd2:51) were sequenced for each sample. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Cells of each cell line (CHLA-03-AA, SJ-GBM2, TP54, SU-DIPG IV) were subcultured and treated as individual cells with vehicle, Delta-24-RGD, ONC201 or the combination of both agents. The next dosages were used to carry out this experiment: Delta-24-RGD (25 MOIs for all cell lines) and ONC201 (CHLA-03-AA: 2 µM; SJ-GBM2: 1.745 µM; TP54: 1.712 µM; SU-DIPG IV: 2 µM). After 48 hours of treatment, cells were collected and frozen at -80 °C. At least three biological replicates were performed for each cell line. Then, we proceeded to isolate total RNA.

value: SU-DIPG IV

value: DMG


title: WA088 GFP GC

value: AAV-EGFP


title: WA087 GFP GC

value: GC


title: DIPGIV_D24RGDONC201_3

value: D24RGD + ONC201


title: H3K36ME3 Cut&Tag of LCLs, NA19128

value: Lymphoblastoid cell lines (LCLs)


title: DIPGIV_D24RGD_3


title: H3K36ME3 Cut&Tag of LCLs, NA19140


title: H3K36ME3 Cut&Tag of LCLs, NA19127


title: F. columnare challenge hour4 white bass rep3 gill tissue


title: WA086 GFP GC


title: DIPGIV_C_3

value: Control


title: DIPGIV_D24RGDONC201_2


title: H3K36ME3 Cut&Tag of LCLs, NA19122


title: DIPGIV_ONC201_2


title: DIPGIV_D24RGD_2


title: DIPGIV_C_2


title: H3K36ME3 Cut&Tag of LCLs, NA19121


title: WA084 GFP GC


title: DIPGIV_D24RGDONC201_1


title: WA083 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA19118


title: DIPGIV_D24RGD_1


title: DIPGIV_ONC201_1


title: H3K36ME3 Cut&Tag of LCLs, NA19119


title: DIPGIV_C_1


title: SJGBM2_D24RGDONC201_3

value: pHGG


title: H3K36ME3 Cut&Tag of LCLs, NA19117


title: SJGBM2_ONC201_3


title: H3K36ME3 Cut&Tag of LCLs, NA19114


title: SJGBM2_C_3


title: WA081 GFP GC


title: SJGBM2_D24RGD_3


title: SJGBM2_D24RGDONC201_2


title: H3K36ME3 Cut&Tag of LCLs, NA19108


title: WA079 GFP GC


title: SJGBM2_ONC201_2


title: H3K36ME3 Cut&Tag of LCLs, NA19107


title: SJGBM2_C_2


title: WA078 GFP GC


title: WA085 GFP GC


title: SJGBM2_D24RGD_2


title: SJGBM2_D24RGDONC201_1


title: H3K36ME3 Cut&Tag of LCLs, NA19102


title: SJGBM2_ONC201_1


title: SJGBM2_D24RGD_1


title: WA082 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA19101


title: WA077 GFP GC


title: SJGBM2_C_1


title: H3K36ME3 Cut&Tag of LCLs, NA19098


title: TP54_D24RGDONC201_4


title: WA076 GFP GC


title: WA075 GFP GC


title: TP54_ONC201_4


title: WA080 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA19096


title: TP54_D24RGD_4


title: TP54_D24RGDONC201_3


title: WA074 GFP GC


title: TP54_C_4


title: H3K36ME3 Cut&Tag of LCLs, NA19095


title: TP54_D24RGD_3


title: TP54_ONC201_3


title: H3K36ME3 Cut&Tag of LCLs, NA19093


title: WA073 GFP GC


title: TP54_C_3


title: TP54_D24RGDONC201_2


title: WA072 GFP GC


title: WA071 GFP GC


title: TP54_D24RGD_2


title: H3K36ME3 Cut&Tag of LCLs, NA19092


title: H3K36ME3 Cut&Tag of LCLs, NA18934


title: TP54_ONC201_2


title: TP54_C_2


title: WA070 GFP GC


title: WA069 GFP GC


title: TP54_ONC201_1


title: TP54_D24RGDONC201_1


title: TP54_D24RGD_1


title: H3K36ME3 Cut&Tag of LCLs, NA18923


title: H3K36ME3 Cut&Tag of LCLs, NA18924


title: WA068 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA18917


title: CHLA03_ONC201_3


title: TP54_C_1


title: H3K36ME3 Cut&Tag of LCLs, NA18915


title: WA067 GFP GC


title: CHLA03_D24RGDONC201_3


title: CHLA03_D24RGDONC201_2


title: WA066 GFP GC


title: CHLA03_ONC201_2


title: CHLA03_D24RGD_3


title: CHLA03_C_3


title: CHLA03_C_2


title: WA065 GFP GC


title: CHLA03_D24RGD_2


title: H3K36ME3 Cut&Tag of LCLs, NA18910


title: CHLA03_D24RGDONC201_1


title: WA063 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA18912


title: CHLA03_ONC201_1


title: WA064 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA18909


title: CHLA03_D24RGD_1


title: WA062 GFP GC


title: H3K36ME3 Cut&Tag of LCLs, NA18907


title: YFP unbound [21102201_201_unbound_S3]

city: Hershey

first: Daniela

last: Zarnescu

state: PA

address: 500 University Drive Crescent Building C4605

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description:
50:50 males and females
21102201_201_unbound_S3

data_processing:
fastq files were generated using bcl2fastq v2.19.1.403
Reads were trimmed with cutadapt v2.7
Trimmed fastqs were aligned to the Dmel genome with STAR v2.6.1d using the following parameters: --runMode alignReads --outSAMtype BAM Unsorted --outSAMmode Full --outSAMstrandField intronMotif --outFilterType BySJout --outSAMunmapped Within --outSAMmapqUnique 255 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignMatesGapMax 1000000 --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 18 --alignSJDBoverhangMin 18 --chimSegmentMin 18 --chimJunctionOverhangMin 18 --outSJfilterOverhangMin 18 18 18 18 --alignTranscriptsPerReadNmax 50000
Aligned reads were counted with featureCounts v1.6.3 using the genome annotation dmel-6.27
.txt files produced for individual samples were aggregated into a single .txt file using python
Assembly: Dmel genome
Supplementary files format and content: A single tab delimited .txt file containing raw counts for each sample

organism: Drosophila melanogaster

source_name: Whole head

extract_protocol:
TRIzol RNA isolation was performed on three biological replicates of IPs from YFP, TDPWT YFP, and TDPG298S YFP from mushroom bodies. RNA was quantified by nanodrop to bring it within range for ribogreen quantification of 0.15625 and 10 ng/ul. RNA was also checked using Agilent Tapestation High Sensitivitiy RNA screentape. 1 ng total RNA was used for SMART Seq HT PLUS (Takara Bio USA, Inc. Cat #R400748) following manufacturer’s protocol. Determination of cDNA quality and quantity was determined via Agilent Tapestation High Sensitivity D5000 Screentape and Qubit dsDNA HS assay for input into library amplification.
Libraries were quantified by Agilent Tapestaion High Sensitivity D1000 Screentape and Kapa Library Quantification kit for Illumina platforms. Libraries were pooled equimolarly, pools were quantified by Agilent Tapestation High Sensitivity D1000 Screentape and Kapa Library Quantification kit and loaded on the NovaSeq 6000 S4 flowcell and sequenced to 101 x 11 x 11 x 101 cycles.

value: Whole head

value: Mushroom body Kenyon cells

tag: Sex

value: pooled male and female

value: Day 1 - 3

value: yw;;P[UAS-2XEYFP]AH3 (GRYFP-5)

tag: developmental stage

value: adult


title: YFP unbound [21101901_901_unbound_S14]

description:
50:50 males and females
21101901_901_unbound_S14


title: H3K36ME3 Cut&Tag of LCLs, NA18881


title: YFP IP [21102201_201_IP_S13]

description:
50:50 males and females
21102201_201_IP_S13


title: YFP unbound [21101902_902_unbound_S10]

description:
50:50 males and females
21101902_902_unbound_S10


title: WA061 GFP GC

value: hippocampal neurons


title: H3K36ME3 Cut&Tag of LCLs, NA18913


title: H3K36ME3 Cut&Tag of LCLs, NA18879


title: YFP IP [21101902_902_IP_S24]

description:
50:50 males and females
21101902_902_IP_S24


title: YFP IP [21101901_901_IP_S7]

description:
50:50 males and females
21101901_901_IP_S7


title: WA056 Ascl4 GC


title: YFP input [21102201_201_input_S20]

description:
50:50 males and females
21102201_201_input_S20


title: H3K36ME3 Cut&Tag of LCLs, NA18877


title: YFP input [21101902_902_input_S23]

description:
50:50 males and females
21101902_902_input_S23


title: WA055 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18876


title: TDP-43 WT unbound [21102202_202_unbound_S25]

description:
50:50 males and females
21102202_202_unbound_S25

value: w; UAS TDP43WT-YFP, UAS mCD8-RFP II (TDP-92)


title: WA054 Ascl4 GC


title: TDP-43 WT unbound [21101505_505_unbound_S6]

description:
50:50 males and females
21101505_505_unbound_S6


title: YFP input [21101901_901_input_S26]

description:
50:50 males and females
21101901_901_input_S26


title: CHLA03_C_1


title: H3K36ME3 Cut&Tag of LCLs, NA18870


title: TDP-43 WT unbound [21101502_502_unbound_S19]

description:
50:50 males and females
21101502_502_unbound_S19


title: H3K36ME3 Cut&Tag of LCLs, NA18868


title: WA053 Ascl4 GC


title: TDP-43 WT IP [21101505_505_IP_S18]

description:
50:50 males and females
21101505_505_IP_S18


title: WA052 Ascl4 GC


title: WA057 Ascl4 GC


title: TDP-43 WT IP [21101502_502_IP_S5]

description:
50:50 males and females
21101502_502_IP_S5


title: H3K36ME3 Cut&Tag of LCLs, NA18867


title: TDP-43 WT input [21101502_502_input_S12]

description:
50:50 males and females
21101502_502_input_S12


title: WA051 Ascl4 GC


title: WA050 Ascl4 GC


title: TDP-43 WT input [21102202_202_input_S27]

description:
50:50 males and females
21102202_202_input_S27


title: H3K36ME3 Cut&Tag of LCLs, NA18864


title: TDP-43 WT input [21101505_505_input_S2]

description:
50:50 males and females
21101505_505_input_S2


title: TDP-43 G298S unbound [21101506_506_unbound_S21]

description:
50:50 males and females
21101506_506_unbound_S21

value: w; UAS TDP43G298S-YFP, UAS mCD8-RFP II (TDP-94)


title: H3K36ME3 Cut&Tag of LCLs, NA18862


title: TDP-43 G298S unbound [21102203_203_unbound_S9]

description:
50:50 males and females
21102203_203_unbound_S9


title: H3K36ME3 Cut&Tag of LCLs, NA18861


title: WA049 Ascl4 GC

description:
Data-no_QC-counts.tsv
Data-counts.tsv
Data-normed.tsv


title: TDP-43 G298S unbound [21101503_503_unbound_S1]

description:
50:50 males and females
21101503_503_unbound_S1


title: WA048 Ascl4 GC


title: TDP-43 WT IP [21102202_202_IP_S22]

description:
50:50 males and females
21102202_202_IP_S22


title: TDP-43 G298S IP [21102203_203_IP_S17]

description:
50:50 males and females
21102203_203_IP_S17


title: TDP-43 G298S IP [21101506_506_IP_S11]

description:
50:50 males and females
21101506_506_IP_S11


title: TDP-43 G298S input [21102203_203_input_S15]

description:
50:50 males and females
21102203_203_input_S15


title: TDP-43 G298S IP [21101503_503_IP_S4]

description:
50:50 males and females
21101503_503_IP_S4


title: TDP-43 G298S input [21101506_506_input_S16]

description:
50:50 males and females
21101506_506_input_S16


title: WA046 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18855


title: WA047 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18858


title: TDP-43 G298S input [21101503_503_input_S8]

description:
50:50 males and females
21101503_503_input_S8


title: H3K36ME3 Cut&Tag of LCLs, NA18853


title: WA045 Ascl4 GC


title: UBXN9-2

city: Shanghai

first: Li

last: Zhang

address: Dongchuan road 800

institute: Shanghai Cancer Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by filtering ofadaptor sequences, low-quality sequences, or rRNAs sequences from the original reads using Seqtk (https://github.com/lh3/seqtk)
paired-end clean reads were aligned to the reference genome using Hisat2 v2.1.0
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38.p6

source_name: LPC-HRas

growth_protocol: LPC-HRas cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted by TRIzol and subjected to RNA-seq analysis. 1ug of total RNA was used for the construction of sequencing libraries.
Total RNA samples in each experiment were subjected to Shanghai Biotechnology Corporation (Shanghai, China) for sequencing. Libraries were made by using TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to Illumina’s instructions and then sequenced on the Illumina HiSeq 2500 system (Illumina, San Diego, CA) according to Illumina’s instructions and then sequenced on the Illumina HiSeq 2500 system (Illumina, San Diego, CA).

value: LPC-HRas

value: liver cancer cells

value: unstimulated


title: H3K36ME3 Cut&Tag of LCLs, NA18852


title: CON-1

value: control


title: TRM_c13_15

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

data_processing:
Pipeline: Reads were processed using snakemake pipelines as indicated under (https://gitlab.lrz.de/ImmunoPhysio/bulkSeqPipe). Parameters are provided in the configuration (see "config.yaml").
Filtering: Reads were filtered using Trimmomatic v0.36.
Mapping: STAR v2.5.3a was used for mapping to annotation release #91 and genome build #38 from Mus musculus (Ensembl). Multimapped reads were discarded.
Differential expression: DESeq2 v1.24.0 was used for differential expression analysis. Differences with a Basemean > 50, an absolute log2 fold change >1, an adjusted p value <0.05 and more than 10 counts in at least 2 samples were considered significant.
Assembly: GRCm38 (release 91)
Supplementary files format and content: The .tsv files contain the read counts for each gene (rows) in each sample (columns).

source_name: liver

extract_protocol:
TotalRNA was isolated using the RNAdvance Cell v2 kit (Beckmann-Coulter). Quality and quantity of isolated RNA was analyzed with the Bioanalyzer RNA Pico Chip (Agilent).
cDNA synthesis was performed with the SMART-Seq v4 Ultra Low Input RNA kit (Takara) following the manufacturers protocol with 12 cycles of PCR amplification. Input amount were 1ng of each RNA sample. cDNA was measured with Bioanalyzer DNA HS Chip (Agilent) and 300pg of amplified cDNA were used for library preparation with the Nextera XP DNA library Preparation Kit (Illumina).  Libraries were analyzed with a Bioanalyzer DNA HS Chip (Agilent) and quantified by qPCR following guidelines from Illumina and using Kapa SYBR mastermix (Kapa Biosystems). After the normalization of all libraries to 2nM, 13 samples each were pooled and sequenced on two single-end runs (1x100bp, dual-index) on a HiSeq2500 (Illumina) using HiSeq Rapid v2 chemistry (Illumina). Demultiplexing was done with the bcl2fastq software (v2.20.0.422).

treatment_protocol: P14 cells were transferred to C57BL/6 mice and infected one day later with either LCMV Clone 13 or LCMV Armstrong. Resident (CD69+CD101+CXCR6+CX3CR1-) and non resident (CX3CR1+) P14 cells from the liver were sorted 27 dpi.

value: liver

value: P14 cells

value: CD8+ T cells

tag: infection

tag: subpopulation

value: TRM

tag: markers

tag: batch

tag: mouse

tag: ID


title: UBXN9-1


title: WA042 Ascl4 GC

tag: tissue

value: GC


title: WA044 Ascl4 GC

tag: genotype


title: H3K36ME3 Cut&Tag of LCLs, NA18523

value: Lymphoblastoid cell lines (LCLs)


title: nonTRM_c13_15

value: nonTRM


title: CON-2

tag: treatment


title: H3K36ME3 Cut&Tag of LCLs, NA18520

tag: cell type


title: nonTRM_c13_14

tag: cell line


title: WA041 Ascl4 GC


title: WA043 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18522


title: nonTRM_c13_13


title: TRM_c13_13


title: H3K36ME3 Cut&Tag of LCLs, NA18519


title: H3K36ME3 Cut&Tag of LCLs, NA18516


title: H3K36ME3 Cut&Tag of LCLs, NA18511


title: TRM_c13_11


title: TRM_c13_12


title: nonTRM_c13_12


title: WA039 Ascl4 GC


title: WA040 Ascl4 GC


title: nonTRM_Arm_4

value: Arm


title: H3K36ME3 Cut&Tag of LCLs, NA18510


title: TRM_Arm_2


title: WA038 Ascl4 GC


title: WA037 Ascl4 GC


title: TRM_c13_14


title: cochlear and vestibular HCs, DMDO47 Hom

city: Bethesda

first: Ronna

last: Hertzano

state: Maryland

address: 35 Convent Drive, Building 35A Room 1F127

department: Neurotology Branch

institute: NIDCD/NIH

data_processing:
Quality of Fastq files was evaluated with FastQC. Reads were aligned to the mouse genome (Mus_musculus.GRCm38) using HiSat (version HISAT2-2.0.4)  and the number of reads that aligned to the coding regions were determined using HTSeq.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cochlear and vestibular hair cells

extract_protocol:
RNA was extracted from sorted cochlear and vestibular HCs using the Direct-zol RNA MiniPrep Kit (Zymo Research). First, TRIzolTM LS (InvitrogenTM) was added to each sample of HCs to 70% of total volume. All following steps were conducted as outlined in the Direct-zol RNA MiniPrep Kit protocol, eluting RNA in 25µL of nuclease free water in the final step.
Libraries were prepared from 2.75-5.43ng of RNA from each sample using the NEBNext Ultra Directional RNA Kit per manufacturer’s instructions with a total of 22 PCR cycles, except for a 5-minute fragmentation time instead of 15 minutes and a SPRI bead size selection before PCR.

value: cochlear and vestibular hair cells

value: Mir96Dmdo Homozygous Mutant- Mir96Dmdo/Dmdo; Atoh1/nGFP+

tag: age


title: H3K36ME3 Cut&Tag of LCLs, NA18508


title: H3K36ME3 Cut&Tag of LCLs, NA18507


title: nonTRM_Arm_2


title: WA036 Ascl4 GC

value: hippocampal neurons


title: cochlear and vestibular HCs, DMDO46 Hom


title: TRM_Arm_1


title: WA035 Ascl4 GC


title: cochlear and vestibular HCs, DMDO43 Hom


title: nonTRM_Arm_1


title: nonTRM_c13_11


title: cochlear and vestibular HCs, DMDO51 Het


title: H3K36ME3 Cut&Tag of LCLs, NA18504


title: cochlear and vestibular HCs, DMDO48 Het


title: WA033 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18502


title: WA034 Ascl4 GC


title: H460 cells,NDI1, IACS, Rep3

city: Dallas

first: Ralph

last: DeBerardinis

address: 6000 Harryhines Blvd

department: CRI

institute: UT Southwestern Medical Center

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to hg19 reference genome by STAR v. 2.5.2b with the following parameters: --runThreadN 28 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outWigStrand Unstranded  --quantMode TranscriptomeSAM.
Genic read counts were derived using HTSeq with parameter “-s no” and normalized by DESeq.
Assembly: hg19
Supplementary files format and content: text file of FPKM value.

growth_protocol: H460 cells were maintained in RMPI with 2.05mM glutamine and 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific, 15596018) and RNeasy Mini kit (Qiagen, 74106)
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, E7490L, E7760L) according to manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or 25nM IACS-010759

value: Non-small cell lung cancer

value: Overexpress NDI1


title: TRM_Arm_4


title: cochlear and vestibular HCs, DMDO45 Het


title: H460 cells,NDI1, IACS, Rep2


title: WA032 Ascl4 GC


title: H3K36ME3 Cut&Tag of LCLs, NA18498


title: H460 cells, NDI1, IACS, Rep1


title: H460 cells,NDI1, DMSO Rep3

value: DMSO


title: WA030 Ascl4 GC


title: cochlear and vestibular HCs, DMDO55 WT

value: Wildtype-Mir96+/+; Atoh1/nGFP+


title: H3K36ME3 Cut&Tag of LCLs, NA18497


title: H3K36ME3 Cut&Tag of LCLs, NA18505


title: H460 cells,NDI1, DMSO Rep2


title: H460 cells, NDI1, DMSO Rep1


title: H3K36ME3 Cut&Tag of LCLs, NA18486


title: WA029 Ascl4 GC


title: WA028 Ascl4 GC


title: RESUB-CTB22131R-TSCMa-p16

city: Raleigh

first: Balaji

middle: M

last: Rao

state: North Carolina

address: Partners II, 840 Main Campus Drive, Room 3107, Raleigh, North Carolina 27606

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
CLC Genomics Workbench (version 23.0.2, QIAGEN Digital Insights) was used
The trimmed sequences were mapped to the reference genome, GRCh38.110 using the RNA-Seq analysis feature in the CLC Genomics Workbench.
The imported reads were trimmed based on quality score and ambiguous nucleotides were also removed using default software settings.
Assembly: GRCh38.110
Supplementary files format and content: Output from CLC workbench after performing RNA seq analysis. These files contain  Name, Chromosome, Region, Expression value, TPM,RPKM,Exons,Gene ID,Gene length, ENSEMBL,Biotype,Unique gene reads,Total gene reads,Transcripts annotated,Uniquely identified transcripts,Exon length,Unique exon reads,Total exon reads,Ratio of unique to total (exon reads) Unique exon-exon reads Total exon-exon reads Unique intron reads Total intron reads Ratio of intron to total gene reads

source_name: Term placenta

extract_protocol:
Purelink RNA Mini Kit (Thermofischer) following manufacturer’s protocol.
The RNA samples were measured using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) to determine their quantity, and their integrity was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina, following the instructions provided by the manufacturer (NEB, Ipswich, MA, USA). In summary, mRNAs were originally concentrated using Oligod(T) beads.
The mRNAs were subjected to fragmentation by heating them at a temperature of 94 °C for a duration of 15 minutes. Subsequently, the first strand and second strand cDNA were produced. The cDNA fragments underwent end repair and adenylation at their 3' ends. Universal adapters were then attached to the cDNA fragments. This was followed by the insertion of indexes and library enrichment by PCR with a limited number of cycles. The sequencing library underwent validation using the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and was quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were combined and distributed into a flowcell on the Illumina HiSeq 4000 instrument or a comparable device, following the instructions provided by the manufacturer. The samples underwent sequencing using a 2x150bp Paired End (PE) arrangement. The HiSeq Control Software (HCS) was used to do image analysis and base calling. The raw sequence data obtained from Illumina HiSeq, in the form of .bcl files, was transformed into fastq files and then de-multiplexed using the Illumina bcl2fastq 2.20 software. One discrepancy was permitted for the identification of index sequences.

value: Term placenta

value: primary

value: wild type


title: H460 cells, control, IACS, Rep3

value: Empty vector control


title: WA027 Ascl4 GC


title: primary osteosarcoma lesion, Metastasis

first: Yujing

address: 600 Yishan Road, Xuhui District

department: Department of Oncology

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
The fastq files of the raw data and feature matrices were obtained using CeleScope (v1.7.1). Subsequently, the data underwent processing using the R package Seurat (version 4.0.4). Filtering was performed to exclude low quality cells, defined as those with minimum expression cells greater than 3, gene numbers less than 200 or greater than 4000, and mitochondrial genes exceeding 15%. Following normalization of gene expression  measurements, batch effects were eliminated using Harmony.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every cell in each sample

source_name: bone

extract_protocol:
Fresh tumor tissue from primary osteosarcoma was immersed in a 10 cm dish filled with GEXSCOPETM tissue preservation solution (Singleron, China) and subsequently chilled on ice for processing. The samples were subjected to three washes with Hanks' Balanced Salt Solution (HBSS; Gibco, USA), followed by fragmentation into 1-2 mm tissue fragments. Surgical forceps were employed to eliminate connective tissue and evident necrotic tissue. Tissue fragments were digested using 2 mL of GEXSCOPETM tissue dissociation solution (Singleron, China) at a temperature of 37 °C with agitation for a duration of 15 minutes. The resulting samples were then filtered through a 40μm sterile filter and centrifuged at a speed of 800 × g for a period of 5 minutes. The supernatant was discarded,and the cell pellet was resuspended in 1 mL of phosphate-buffered saline (PBS; Gibco, USA). To remove erythrocytes, 2 mL of GEXSCOPETM  erythrocyte lysis buffer (Singleron, China) was promptly added. The cell suspension was subjected to incubation at a temperature of 25 °C for a duration of 10 minutes, followed by centrifugation at a force of 500 × g for a period of 5 minutes. The resulting pellet was then resuspended in phosphate-buffered saline (PBS). Subsequently, the samples were stained with trypan blue (Gibco, USA) and the viability of the cells was evaluated using phase contrast light microscopy (Olympus, Japan).
For the loading of single-cell suspensions (2×10^5 cells/mL) onto the microwell chip, PBS (Gibco, USA) was employed in conjunction with the Singleron Matrix® Single Cell Processing System. The Barcoding Beads are retrieved from the microwell chip, and subsequently subjected to reverse transcription of the mRNA that has been captured by the Barcoding Beads, resulting in the generation of complementary DNA (cDNA). The cDNA is then amplified through polymerase chain reaction (PCR). Following amplification, the cDNA is  fragmented and joined with sequencing adapters. The construction of scRNA-seq libraries adhered to the GEXSCOPE® Single Cell RNA Library Kits (Singleron, China) protocol. Each individual library was diluted to a concentration of 4 nM, pooled together, and subjected to sequencing on an Illumina novaseq 6000 platform, utilizing 150 bp paired end reads.

value: bone

value: osteosarcoma

tag: phenotype

value: Metastasis


title: RESUB-CTB22131R-TSCMa-p17


title: primary osteosarcoma lesion, Non-metastasis

value: Non-metastasis


title: H460 cells,control, IACS, Rep2


title: cochlear and vestibular HCs, DMDO59 WT


title: H3K36ME3 Cut&Tag of LCLs, NA18499

value: Lymphoblastoid cell lines (LCLs)

tag: antibody


title: WA031 Ascl4 GC

value: GC


title: H460 cells, control, IACS, Rep1


title: WA025 Ascl4 GC


title: RESUB-CTB21126R--TSCMa-p16


title: WA026 Ascl4 GC


title: RESUB-CTB21126R--TSCMa-p17


title: H460 cells,control, DMSO Rep3


title: YJXQ3

city: Beijing

first: Xuejiao

last: Wang

address: No.5 Beixiange, Xicheng District

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

data_processing:
The transcriptome sequencing was performed on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the Hg38 genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
DESeq2 was used for gene expression analysis.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's instructions.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Peripheral blood mononuclear cells

value: myocardial infarction

value: leukocyte

value: acute stage


title: cochlear and vestibular HCs, DMDO44 WT

value: cochlear and vestibular hair cells


title: H460 cells, control, DMSO Rep2

value: Non-small cell lung cancer

value: DMSO


title: RESUB-CTB22131R--TSCM-fr-TUA-p9-9

value: Term placenta


title: YJXQ2

value: subacute stage


title: H460 cells, control, DMSO Rep1


title: WA023 Ascl4 GC

value: hippocampal neurons


title: WA022 Ascl4 GC


title: RESUB-CTB22131R--TSCM-fr-TUA-p10-9

value: primary

value: wild type


title: YJXQ1


title: H460 cells, parental, IACS, Rep3

value: WT


title: WA021 Ascl4 GC


title: RESUB-CTB22131R--TSCM-fr-TUA-p9-10


title: YJXQ5


title: RESUB-CTB21126R--TSCMa-p12


title: JXQ2


title: YJXQ4


title: JXQ3


title: H460 cells, parental, IACS, Rep1


title: WA019 GFP GC

value: AAV-EGFP


title: RESUB-CTB21126R--TSCM -p7-7


title: RESUB-CTB21126R--TSCM p7-8


title: WA018 GFP GC


title: WA024 Ascl4 GC


title: JXQ1


title: RESUB-CTB21126R--TSCM -p7-11


title: CJQ7

value: old phase of AMI


title: H460 cells, parental, DMSO Rep2


title: WA017 GFP GC


title: CJQ6


title: H460 cells, parental, DMSO Rep1


title: RESUB-CTB22131R--TUA-p21


title: WA016 GFP GC


title: CJQ5


title: WA015 GFP GC


title: CJQ4


title: RESUB-CTB22131R--TUA-p22


title: H460 cells, parental, IACS, Rep2


title: WA020 GFP GC


title: WA014 GFP GC


title: CJQ3


title: RESUB-CTB21126R--TUA-p7


title: SU-DIPG-IV_sgFOSL1_RNAseq_rep1

city: New York

first: Zhiguo

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were aligned to hg19 reference using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019). Overlapped peaks between replicates were retained and then merged to obtain a consensus peak set for each Cut&Run target using BEDTools (version 2.29.2) (Quinlan and Hall, 2010).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR. The P value of each gene was adjusted using the Benjamini–Hochberg (BH) procedure. Genes with a BH-adjusted P value less than 0.05 and a fold change greater than 1.5 (upregulated) or less than 0.67 (downregulated) were considered as differentially expressed genes (DGEs).
Assembly: hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.

source_name: patient-derived cell culture

growth_protocol: Patient-derived DMG cells (SU-DIPG-IV, SU-DIPG-VI, SU-DIPG-XVII, SU-DIPG-XXXVI) were obtained from Dr. Michelle Monje at Stanford University and maintained as neurospheres in knockout DMEM/F12 media (Gibco) supplemented with StemPro Neural Supplement (Gibco), 20 ng/ml human FGF-basic (bFGF) (Gibco), 20 ng/ml human EGF (Gibco), 2 mM L-Glutamine (Gioco), 1% penicillin/streptomycin (Invitrogen) and plasmocin (InvivoGen). Alternatively, the DMG cells were maintained as adherent culture using 24 μg/ml fibronectin-coated dishes. Mouse DMG cells with H3.3K27M mutation were obtained from Dr. Oren Becher at Mount Sinai Hospital and maintained as neurospheres in NeuroCult™ Basal Medium (STEMCELL Technologies) containing Neurocult proliferation supplement (STEMCELL Technologies), 20 ng/ml human bFGF (Gibco), 10 ng/ml human EGF (Gibco), 2 μg/mL Heparin (STEMCELL Technologies) and 1% penicillin/streptomycin (Invitrogen). All cells were cultured at 37℃ with 5% CO2, and were periodically tested mycoplasma negative by PCR.

extract_protocol:
CUT&RUN was performed as previously described (Skene and Henikoff, 2017) with minor modifications. Total RNA samples were purified the same as for RT-PCR.
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. CUT&RUN libraries were prepared using ACCEL-NGSTM 1S plus DNA library kit and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: FOSL1 KO


title: CJQ2

value: Peripheral blood mononuclear cells


title: SU-DIPG-IV_WT1_RNAseq


title: RESUB-CTB21126R--TUA-p8


title: SU-DIPG-IV_WT2_RNAseq


title: WA012 GFP GC

value: GC


title: H460 cells, parental, DMSO Rep3


title: SU-DIPG-XXXVI_sgCHD2_RNAseq_rep2

value: CHD2 KO


title: RESUB-CTB22131R+ TUA p12 v1


title: WA011 GFP GC


title: CJQ1

value: myocardial infarction

value: leukocyte


title: SU-DIPG-XXXVI_sgCHD2_RNAseq_rep1


title: Intracranial Tissue, Patient 7

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

data_processing:
Sequencing data was aligned to the human genome using 10X Genomics Cell Ranger before importing into Partek Flow Genomics Suite (RRID: SCR_011860) for the remainder of the analysis.
A standard quality control pipeline was implemented to safeguard against contamination by low-quality cells/reads.
Resulting single-cell count matrices were normalized within Partek Flow using counts per million, add 1, and log base 2 transformed. Samples were then integrated for all downstream analyses.
Assembly: GRCh38-2020-A
Supplementary files format and content: Hierarchical Data Format .h5 files containing count matricies for each sample

source_name: Intracranial Tissue

extract_protocol:
Residual tissues and paired blood samples were collected intraoperatively from patients undergoing craniotomy with debridement for infection treatment after informed consent (IRB #0241-18-EP).  Blood was used as an intrapatient comparator for tissue analysis. Leukocytes were isolated from whole blood using Histopaque, and the resulting plasma layer was collected and frozen for subsequent cytokine/chemokine analysis. The resulting cells were washed with 1X PBS and filtered through a filter-top FACS tube before flow cytometry staining. Tissue samples were homogenized in HBSS with 10% FBS and passed through a 70 μm filter to achieve a single-cell suspension. Samples were centrifuged, supernatant collected for cytokine/chemokine measurements, and cells washed in 1X PBS before RBC lysis. Bone flaps were submerged in 1X PBS and vortexed for 1 min to dislodge adherent cells, which were collected and filtered through a 70 μm filter to remove aggregates. Single cell suspensions were stained for CD45-APC-Cy7 (RRID:AB_312981) and Zombie UV Fixable Viability Kit (BioLegend) and FACS sorted to obtain live CD45+ leukocytes. Samples were evaluated using a Luna automated fluorescent cell counter (Logos Biosystems) to assess cell viability, density, and debris before single-cell capture with a 10X Genomics instrument. Cells were then lysed, and the resulting DNA was reverse-transcribed and barcoded using a Chromium Single Cell 3’ Reagent Kit (v3.1; 10X Genomics) according to the manufacturer's instructions.
Illumina-compatible cDNA libraries were quantified with a Qubit-30 Fluorometer and assessed using a fragment analyzer before loading on a Novaseq6000 instrument at a final concentration of 300pM for generation of 75 bp pair-end reads. Samples sequenced included: patient 7 blood (5215 cells), bone flap (2957 cells), epidural (3459 cells), and intracranial tissue (ICT; 2982 cells); patient 11 blood (3925 cells), bone flap (5583 cells), and subgalea/epidural tissues (4374 cells); patient 14 blood (3645 cells), subgalea (626 cells), and bone flap (2973 cells) tissues; patient 15 blood (16983 cells), epidural (7125 cells), subgalea (4206 cells), and bone flap (7360 cells) tissues. Sequencing was performed to an average depth of 50,000-100,000 reads per cell

value: Intracranial Tissue

value: Patient 7


title: SU-DIPG-IV_sgFOSL1_RNAseq_rep2


title: WA010 GFP GC


title: SU-DIPG-XXXVI_WT_RNAseq


title: WA009 GFP GC


title: Dura, Patient 7

source_name: Dura

value: Dura


title: Bone Flap, Patient 7

source_name: Bone Flap

value: Bone Flap


title: WA008 GFP GC

value: hippocampal neurons


title: WA013 GFP GC


title: Control Subject 37

city: Tel Aviv

first: Avraham

last: Unterman

address: Weizmann 6

country: Israel

institute: Tel Aviv Sourasky Medical Center

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline (v3.0.2) to create FASTQ files. Next, Cell Ranger count pipeline (v3.0.2) was employed in order to perform alignment (using STAR), filtering, barcode counting and UMI counting.
Seurat R package (v3.1) was used for all downstream analyses. 10x Genomics gene expression aggregated matrix was converted into a Seurat object using CreateSeuratObject function. Genes expressed by fewer than 3 cells were filtered out. Cells with mitochondrial gene percentages higher than 12% and cells with fewer than 1000 Unique Molecular Identifiers (UMIs) were excluded from the study to filter out dead and dying cells.
Assembly: GRCh38
Supplementary files format and content: For each sample, processed data include Cell Ranger Count filtered outputs: cell barcodes (barcodes.tsv.gz), genes (features.tsv.gz) and count matrix (matrix.mtx.gz).

source_name: PBMCs

extract_protocol:
PBMCs were isolated from whole blood by density gradient centrifugation using Histopaque 1077 (Sigma Aldrich) and immediately cryopreserved in 70% DMEM, 20% FBS and 10% DMSO. PBMCs were later thawed and DMSO was removed by 5 serial dilutions in cold growth medium added at 1:1 ratio, followed by cetrifugation and removal of suprenatant. Then, cell pellets were resuspended in PBS + 0.04% BSA, filtered using a 40 micron strainer, counted and loaded to the 10x chromium platform. To minimize batch effects, samples were processed in five randomized and balanced batches of 8, each containing 2-3 samples of each of the 3 patient categories: stable IPF, progressive IPF, and controls. The division into batches can be found in Table E1 in the online manuscript.
Cells from each sample were loaded onto the 10x Chromium Chip A, according to the manufacturer’s user guide (Chromium Single Cell V(D)J Reagent Kits User Guide, document number CG000086, revision J, November 2018), aiming for recovery of 10,000 cells per lane. The loaded Chip A was placed in 10x Chromium Controller to create Gel Beads-in-emulsion (GEMs). The next steps were carried out according to the manufacturer’s user guide, including GEM-RT incubation, post GEM-RT Dynabead cleanup, cDNA amplification and cleanup, fragmentation, end-repair and A-tailing, adaptor ligation, sample Index PCR and double-sided size selection using SPRIselect (Beckman Coulter).

value: PBMCs

tag: group assignment

value: Control

tag: age (years)

value: Female

tag: race/ethnicity

value: Caucasian

tag: smoking

value: Never

tag: pack years

tag: dlco% predicted

tag: fvc% predicted


title: Blood, Patient 7

source_name: Blood

value: Blood


title: WA007 GFP GC

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned to Ensembl GRCm38 reference transcriptome (Version-86), using the STAR aligner with the following parameters: trimLeft = 10, minTailQuality = 15, minAverageQuality = 20 and minReadLength = 30. Gene counts were calculated using HTSeq  (Data-no_QC-counts.tsv and Data-counts.tsv)
Cells that passed quality control were normalized (Data-normed.tsv)
Differential gene expression was analyzed using edgR.
Assembly: GRCm38.p4
Supplementary files format and content: Data-no_QC-counts.tsv; raw counts, all cells
Supplementary files format and content: Data-counts.tsv; raw counts, cells passed QC
Supplementary files format and content: Data-normed.tsv; normalized counts, cells passed QC

source_name: hippocampal neurons

extract_protocol: single cell extraction via patch pipette (patch-RNAseq)

value: AAV-EGFP


title: RESUB-CTB21126R--TUA-p9

value: Term placenta

value: primary

value: wild type


title: Control Subject 36

tag: Sex

value: Male

value: Ever


title: Epigalea, Patient 15

source_name: Epigalea

value: Epigalea

value: Patient 15


title: SU-DIPG-XVII_sgCHD2_RNAseq_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: CHD2 KO


title: WA006 GFP GC

value: hippocampal neurons

value: GC


title: Subgalea, Patient 15

source_name: Subgalea

value: Subgalea


title: Control Subject 40

value: PBMCs

value: Control


title: SU-DIPG-XVII_WT_RNAseq_rep1

value: WT


title: Control Subject 35

value: Caucasian


title: SU-DIPG-XVII_WT_RNAseq_rep2


title: Bone Flap, Patient 15

value: Bone Flap


title: WA005 GFP GC

value: AAV-EGFP


title: SU-DIPG-IV_sgCHD2_RNAseq_rep2


title: Control Subject 39

value: Never


title: WA004 GFP GC


title: Control Subject 33


title: WA003 GFP GC


title: Control Subject 34

value: Female


title: Control Subject 32

value: Male


title: Blood, Patient 15

value: Blood


title: Control Subject 38


title: SU-DIPG-XVII_sgCHD2_RNAseq_rep2


title: SU-DIPG-IV_sgCHD2_RNAseq_rep1


title: Subgalea, Patient 14

value: Patient 14


title: SU-DIPG-IV_WT_RNAseq_rep2


title: WA002 GFP GC


title: Control Subject 31


title: Bone Flap, Patient 14


title: SU-DIPG-IV_WT_RNAseq_rep1


title: WA001 GFP GC


title: Blood, Patient 14


title: PAB_3

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3;WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: mm10
Supplementary files format and content: FPKM

source_name: right ventricle

growth_protocol: Mice live with their mother under 19-22℃ with free access to food and water

extract_protocol:
Right ventricular tissue was rapidly removed from executed rat and flash frozen in -80℃ refrigerator, RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Neonatal mouse (within 24h after birth) were subjected to sham and PAB group, mice in PAB group underwent pulmonary artery banding surgery,  mice in sham group underwent same surgical procedures but without banding

tag: strain

value: right ventricle

value: pulmonary artery banding surgery on postnatal day 1

tag: harvest

value: postnatal day 7


title: Subgalea and Epidural, Patient 11

source_name: Subgalea and Epidural

tag: tissue

value: Subgalea and Epidural

value: Patient 11


title: Control Subject 29

value: Ever